Sean,

Thanks for your email. Does your answer imply that batch effect affects samples from different classes (control, treated) differently? Since there is interaction term between batch effect and treatment effect. 

Thanks again,

James

Sean Davis <sdavis2@mail.nih.gov> wrote: 

On Dec 8, 2007 10:59 AM, James Anderson <janderson_net@yahoo.com> wrote:
 Dear List,

I am now  analyzing some Affy data with obvious batch effect with different dose level, one conceptual question regarding batch effect and treatment effect is that does the batch effect affect control or treated samples differently? 

You could fit a linear model that includes treatment effect, batch effect, and an interaction effect.

Sean




 

       
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